Genome within a Genome

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Tony Rook
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Genome within a Genome

A very interesting study was published online on August 30, 2007 at Science which reported the discovery of a bacterial genome within the genome of fruitfly Drosophila ananassae. The researchers apparently have identified 44 out the 45 genes from a bacterium within the genus Wolbachia within the fly's genome. More interesting is the fact that 28 of these genes are active within the fly's genome.

The author's note that gene sequencing programs may need to be revised, since most of these programs will throw out bacterial genes as mere contaminants.

The big thing that strikes me about this study is the evolutionary adaptation aspect. It seems quite amazing to me that species are able to incorporate entire genes (let alone entire genomes) within their genomes for evolutionary advantages.

To read more about this study...

Link here -
Bacterial genome found within a fly's - DNA transfer from bacteria to animals is more common than thought.
By Ewen Callaway

Original Reference -
Julie C. Dunning Hotopp, et al. Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes. Science, Published Online August 30, 2007. DOI: 10.1126/science.1142490

Abstract:
Although common among bacteria, lateral gene transferthe movement of genes between distantly related organismsis thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of 4 insect and 4 nematode species that range from nearly the entire Wolbachia genome (>1 megabase) to short (<500 base pairs) insertions. Potential Wolbachia to host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.

Jason King
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Isn't this supposed to be how

Isn't this supposed to be how we eukaryotes got our mitochondria?

Tony Rook
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That is a similar yet quite

That is a similar yet quite different mechanism, since this recent study sheds light on how bacterial genomes have been actually incorporated into the genomes of higher species. Mitochondrial adaptation should be considered more along the lines of other extra-nuclear genetic information. This can be related to prokaryotes adaptations through the uptake of plasmid DNA.

Here are some pretty good reference for mitochondrial evolution...

Michael W Gray, Gertraud Burger, and B Franz Lang. The origin and early evolution of mitochondria. Genome Biol. 2001; 2(6): reviews1018.1reviews1018.5

Abstract:
Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial (specifically α-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome.

Michael W. Gray, Gertraud Burger, B. Franz Lang. Mitochondrial Evolution. Science 5 March 1999: Vol. 283. no. 5407, pp. 1476 - 1481. DOI: 10.1126/science.283.5407.1476

Abstract:
The serial endosymbiosis theory is a favored model for explaining the origin of mitochondria, a defining event in the evolution of eukaryotic cells. As usually described, this theory posits that mitochondria are the direct descendants of a bacterial endosymbiont that became established at an early stage in a nucleus-containing (but amitochondriate) host cell. Gene sequence data strongly support a monophyletic origin of the mitochondrion from a eubacterial ancestor shared with a subgroup of the alpha -Proteobacteria. However, recent studies of unicellular eukaryotes (protists), some of them little known, have provided insights that challenge the traditional serial endosymbiosis-based view of how the eukaryotic cell and its mitochondrion came to be. These data indicate that the mitochondrion arose in a common ancestor of all extant eukaryotes and raise the possibility that this organelle originated at essentially the same time as the nuclear component of the eukaryotic cell rather than in a separate, subsequent event.

Paulien Smits, Jan A. M. Smeitink, Lambert P. van den Heuvel, Martijn A. Huynen and Thijs J. G. Ettema. Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Research 2007 35(14):4686-4703; doi:10.1093/nar/gkm441

Abstract:
For production of proteins that are encoded by the mitochondrial genome, mitochondria rely on their own mitochondrial translation system, with the mitoribosome as its central component. Using extensive homology searches, we have reconstructed the evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, revealing an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. We observe large variations in the protein content of mitoribosomes between different eukaryotes, with mammalian mitoribosomes sharing only 74 and 43% of its proteins with yeast and Leishmania mitoribosomes, respectively. We detected many previously unidentified mitochondrial ribosomal proteins (MRPs) and found that several have increased in size compared to their bacterial ancestral counterparts by addition of functional domains. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. Using sensitive profileprofile homology searches, we found hitherto undetected homology between bacterial and eukaryotic ribosomal proteins, as well as between fungal and mammalian ribosomal proteins, detecting two novel human MRPs. These newly detected MRPs constitute, along with evolutionary conserved MRPs, excellent new screening targets for human patients with unresolved mitochondrial oxidative phosphorylation disorders.

Tony Rook
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However to bring the topic

However to bring the topic back to the original post concerning 'Widespread Lateral Gene Transfer', there is a great discussion occurring on The Tree of Life Blog between the evolutionary biologist blogger Jonathan A. Eisen, the authors of this paper - Jack Werren and Julie Dunning Hotopp, along with several blog readers.

The blogger sarcastically gives the authors the Adaptationomics Award for jumping to the conclusion that "just because you can think of an adaptive explanation does not mean your explanation is correct." However, this award is completely in jest. As you read the blog you realize that the authors and the blogger are old colleagues and in fact he really admires the study, which is evident by his comment "And I am giving out my first award in this to Jack Werren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

Parvoman, there is also some interesting discussion concerning the "extensive work on what are called 'numts' (nuclear mitochondrial DNA) in humans and other species"...

Amritha Nair
Amritha Nair's picture
what is the evolutionary

what is the evolutionary significance of horizontal gene transfer?

Tony Rook
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Amritha Nair -

Amritha Nair -

There has been a large influx of recent publications regarding the significance of Horizonital Gene Transfer (HGT) or Lateral Gene Transfer (LGT). Traditional evolutionary theory or classical Darwinian evolution focuses on Vertical Gene Transfer or the process of acquiring genetic material only from the individuals ancestors. HGT or LGT increases evolutionary diversity by compounding additional factor for transferring genetic material from outside ancestral lineages and even outside of the species from which the individual organism has evolved from.

In a recent article published in PNAS, Kechris et al explains the significance and debate of LGT here...

"Lateral gene transfer (LGT) is the process by which genetic material is transferred between distinct evolutionary lineages. This mechanism contrasts with the Darwinian model of vertical descent, where genetic material is inherited from the preceding generation (1). LGT and integration of the transferred DNA into the recipient organisms chromosome occurs by various extensively studied mechanisms (2). LGT is relatively common among prokaryotes, but less common between prokaryotes and eukaryotes. The spread of the acquired gene(s) in the recipient species population depends on natural selection and/or neutral genetic drift. For example, a gene that has been laterally transferred may confer antibiotic resistance and therefore provide a selective advantage to the organism in the presence of the antibiotic. It is evident that LGT may occur frequently at the cellular level, but it is more difficult for a transferred gene to be sustained in the population and subsequent generations (3, 4). It is commonly accepted that LGT is a source of genetic diversity and has important evolutionary consequences, but opinions vary on the degree of its influence on microbial evolution (4). This topic is of great current interest among biologists and many methods for detecting probable LGT occurrences have been developed (for reviews, see refs. 1, 3, and 5)."

Cited Reference:
Katherina J. Kechris, Jason C. Lin, Peter J. Bickel, and Alexander N. Glazer. Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study. PNAS. June 20, 2006, vol. 103, no. 25, 9584-9589.

References Cited within excerpt:
1. Koonin, E. V., Makarova, K. S. & Aravind, L. (2001) Annu.
Rev. Microbiol. 55, 709742.
2. Syvanen, M. & Kado, C. I. eds.Horizontal Gene Transfer
(2002) (Academic, London), 2nd Ed.
3. Kurland, C. G., Canback, B. & Berg, O. G. (2003) Proc. Natl.
Acad. Sci. USA 100, 96589662.
4. Kurland, C. G. (2005) BioEssays 27, 741747.
5. Eisen, J. A. (2000) Curr. Opin. Genet. Dev. 10, 606611.